Test Code | D1310 |
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Test Summary |
STAT diagnostic whole exome and mitochondrial genome sequencing of the proband and 2 family members. |
Turn Around Time | 12 - 14 days |
Acceptable Sample Types | DNA, Isolated , Dried Blood Spots , Saliva , Whole Blood (EDTA) |
Acceptable Billing Types | Institutional Billing , Self (patient) Payment |
NY Approved | Yes |
Self (patient) Price | $3,900.00 |
Institutional Price | $5,000.00 |
CPT Codes** | 81415(x1), 81416(x1), 81479(x2), 81460(x1) |
Whole Exome Sequencing includes:
All variants are analyzed according to American College of Medical Genetics and Genomics (ACMG) guidelines, and pathogenic, likely pathogenic, and variants of uncertain significance (VOUS) are reported. Variant analysis is phenotype-driven to minimize the reporting of VOUS.
Familial testing for VOUS is complimentary for up to two variants in two family members.
Complimentary opt-in for additional reports:
One complimentary reanalysis is included and can be requested at any time.
Access to raw data is included and available via electronic transfer.
This testing includes whole exome sequencing, copy number variant analysis, and mitochondrial genome sequencing. Sequencing is performed on genomic DNA enriched for the exome using a sequence capture method. Direct sequencing of the amplified captured regions was performed using 2X150bp reads on Illumina next-generation sequencing (NGS) systems. A base is considered to have sufficient coverage at 20X and an exon is considered fully covered if all coding bases plus three nucleotides of flanking sequence on either side are covered at 20X or more. A list of low coverage regions, if any, is available upon request. Alignment to the human reference genome (GRCh37) is performed and annotated variants are identified in the targeted region. Variants reviewed have a minimum coverage of 8X and an alternate allele frequency of 20% or higher. Indels and single nucleotide variants (SNVs) may be confirmed by Sanger sequence analysis before reporting at director discretion. Mitochondrial DNA is sequenced and analyzed using the same pipeline. This assay cannot detect variants in regions of the exome that are not covered, such as deep intronic, promoter, and enhancer regions, and areas containing large numbers of tandem repeats. Genes and/or exons located in pseudogene regions are not covered in this assay. Copy number variation (CNV) analysis detects deletions and duplications; in some instances, due to the size of the exons, sequence complexity, or other factors, not all CNVs may be analyzed or may be difficult to detect. When reported, copy number variant size is approximate. Actual breakpoint locations may lie outside of the targeted regions. This assay does not interrogate CNVs in mitochondrial DNA. CNV analysis will not detect tandem repeats, balanced alterations (reciprocal translocations, Robertsonian translocations, inversions, and balanced insertions), methylation abnormalities, triploidy, and genomic imbalances in segmentally duplicated regions. This assay is not designed to detect mosaicism; possible cases of mosaicism may be investigated at the discretion of the laboratory director. Primary data analysis is performed using Illumina bcl2fastq converter v2.19. Secondary analysis is performed using Illumina DRAGEN Bio-IT Platform v.3.10.8. Tertiary data analysis is performed using SnpEff v5.0 and Revvity Omics' internal ODIN v.1.01 software. CNV and absence of heterozygosity are assessed using BioDiscovery’s NxClinical v6.1 software.
Collection | Required DNA Quantity by Test Type*:
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Sample Condition | * Required DNA Quality: High molecular weight DNA (>12kb). A260/A280 reading should be ≥ 1.8. A260/230 a ratio range of 1.8 to 2.2. Contact the laboratory for specific amounts if total ng cannot be met. |
Shipping | Ship overnight at ambient temperature. |
Special Sample Instructions |
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Collection Container(s) | EDTA (purple top) |
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Collection | Infants (< 2-years): 2 to 3 mL; Children (>2-years): 3 to 5 mL; Older children and adults: Minimum 5mL. The blood tube should be inverted several times immediately after blood collection to prevent coagulation. |
Sample Condition | Store at ambient temperature. Do not refrigerate or freeze. |
Shipping | Ship overnight at ambient temperature ensuring receipt within 5-days of collection. |
Special Sample Instructions | Clotted or hemolyzed samples are not accepted. |
Collection Container(s) | Oragene™ Saliva Collection Kit or ORAcollect-Dx kit |
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Collection | Collect saliva on an Oragene™ Saliva Collection Kit ORAcollect-Dx kit according to the manufacturer's instructions. |
Sample Condition | Store at ambient temperature. Do not refrigerate or freeze. |
Shipping | Ship overnight at ambient temperature. |
Special Sample Instructions | Please contact Revvity Omics to request the saliva collection kit for patients who cannot provide a blood sample as whole blood is the preferred sample. Testing using Saliva swabs is currently not available for customers in India. Contact the Revvity Omics laboratory for more information. |
Collection Container(s) | Dried blood spot card |
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Collection | Follow kit instructions. Briefly, allow blood to saturate the card until indicated areas are filled and blood has soaked through the card. Air dry the card at ambient temperature for at least 3 hours.
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Sample Condition | Follow the instructions provided with the collection set. Store the dried blood at ambient temperature for up to two days. If the specimen cannot be sent as soon as it is dry, the filter paper should be placed in a sealable plastic bag and stored in a refrigerator (≤ 8°C) or preferably in a freezer. |
Shipping | Follow kit instructions. Double bag and ship overnight at ambient temperature. |